Steps to reproduce:

• Log In
• Fork via https://pagure.io/pagure/ by clicking "fork"
• Clone fork: git glone ssh://git@pagure.io/forks/$user/pagure.git
• Make changes in the master branch
• git commit -am "create a PR"
• git push origin master
• Go to original project: https://pagure.io/pagure/pull-requests
• Try using "File Pull Request" to create a PR from $user/pagure for the master branch

This is likely just a UI issue as a workaround is to go to https://pagure.io/fork/$user/pagure/commits/master and select to create from there.